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More information about some of these proteins and other proteins motions can be found at the following links:

Although it has been clearly established that a protein is able to undergo conformational changes during the binding process, most docking studies consider the protein as a rigid structure. The reason for this crude approximation is the extraordinary increase in computational complexity that is required to include the degrees of freedom of a protein in a modeling study. There is currently no computationally efficient docking method that is able to screen a large database of potential ligands against a target receptor while considering the full flexibility of both ligand and receptor. In order for this process to become efficient, it is necessary to find a representation for protein flexibility that avoids the direct search of a solution space comprised of thousands of degrees of freedom. What follows is a brief review of the different representations that have been used to incorporate protein flexibility in the modeling of protein/ligand interactions. A common theme behind all these approaches is that the accuracy of the results is usually directly proportional to the computational complexity of the representation. The different types of flexibility representations models are grouped into categories that illustrate some of the key ideas that have been presented in the literature in recent years. However it is important to note that the boundaries between these categories are not rigid and in fact several of the publications referenced below could easily fall in more than one category.

Flexibility representations

Soft receptors

Perhaps the simplest solution to represent some degree of receptor flexibility in docking applications is the use of soft receptors. Soft receptors can be easily generated by relaxing the high energy penalty that the system incurs when an atom in the ligand overlaps an atom in the receptor structure. By reducing the van der Waals contributions to the total energy score the receptor is in practice made softer, thus allowing, for example, a larger ligand to fit in a binding site determined experimentally for a smaller molecule (see Figure 6). The rationale behind this approach is that the receptor structure has some inherent flexibility which allows it to adapt to slightly differently shaped ligands by resorting to small variations in the orientation of binding site chains and backbone positions. If the change in the receptor conformation is small enough, it is assumed that the receptor is capable of such a conformational change, given its large number of degrees of freedom, even though the conformational change itself is not modeled explicitly. It is also assumed that the change in protein conformation does not incur a sufficiently high energetic penalty to offset the improved interaction energy between the ligand and the receptor. The main advantage of using soft receptors is ease of implementation (docking algorithms stay unchanged) and speed (the cost of evaluating the scoring function is the same as for the rigid case).

a) Three dimensional van der Walls representation of a target receptor. b) Close up image of a section of the binding site. For the purposes of rigid protein docking, the receptor is commonly described by the union of the volumes occupied by its atoms. The steric collision of any atom of the candidate ligand with the atoms of the receptor will result in a high energetic penalty. c) Same section of the binding site as shown in b) but with reduced radii for the atoms in the receptor. This type of soft representation allows ligand atoms to enter the shaded area without incurring a high energetic penalty.

Questions & Answers

where we get a research paper on Nano chemistry....?
Maira Reply
nanopartical of organic/inorganic / physical chemistry , pdf / thesis / review
Ali
what are the products of Nano chemistry?
Maira Reply
There are lots of products of nano chemistry... Like nano coatings.....carbon fiber.. And lots of others..
learn
Even nanotechnology is pretty much all about chemistry... Its the chemistry on quantum or atomic level
learn
Google
da
no nanotechnology is also a part of physics and maths it requires angle formulas and some pressure regarding concepts
Bhagvanji
hey
Giriraj
Preparation and Applications of Nanomaterial for Drug Delivery
Hafiz Reply
revolt
da
Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
ya I also want to know the raman spectra
Bhagvanji
I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
I think
Professor
Nasa has use it in the 60's, copper as water purification in the moon travel.
Alexandre
nanocopper obvius
Alexandre
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
Rafiq
if virus is killing to make ARTIFICIAL DNA OF GRAPHENE FOR KILLED THE VIRUS .THIS IS OUR ASSUMPTION
Anam
analytical skills graphene is prepared to kill any type viruses .
Anam
Any one who tell me about Preparation and application of Nanomaterial for drug Delivery
Hafiz
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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